Script introduction
Find in the following lines the code corresponding to the analysis of the article: The European freshwater landscape and hotspot areas of mass effects and regional connectivity.
All the suplementary material images, original scripts and used functions can be found in:
Article DOI: https://doi.org/10.1111/ddi.13711
Direct link to repositpory: https://github.com/Metacommunity-Lab/DD_PanEU_Waterscape
To properly follow the following steps we recommend to read the entire work to better contextualize the use and limitations of the current codes and functions.
The scripts can be found in the following repository
Link to the function: https://github.com/Metacommunity-Lab/DD_PanEU_Waterscape
Link to supplementary material: https://doi.org/10.1111/ddi.13711
The following lines of script correspond to the results obtained and the maps generation of the following paper: Cunillera-Montcusí, D., J. Bou, T. Mehner, S. Brucet, M. Arim, & A. I. Borthagaray, 2023. The European freshwater landscape and hotspot areas of mass effects and regional connectivity. Diversity and Distributions 29: 997–1008.
The current database includes all the generated observaitons of different centrality metrics corresponding to 3 main centrality metrics distributed in cells fo 10x10 km throghout the entire European continent. Once the weighted graph was defined, three centrality metrics were estimated for each cell (node).
The metric ‘out-degree’ that reflects the potential of a node (local communities) to operate as a source community is the sum of link weights along all the links that start on the reference cell.
The metric ‘in-degree’, which reflects the importance of incoming dispersal from other communities for local diversity, is estimated as the sum of all links arriving at the reference cell.
Additionally, local communities’ importance for connecting other communities (corridor effects) is captured by the graph centrality metric ‘betweenness’. This metric indicates the number of pairs of other communities that pass through this community in the shortest path that connects them.
In-degree, out-degree and betweenness were estimated for each of the 134,244 spatial cells of Europe. All the analyses were performed for all freshwaters combined and for ephemeral, temporal and permanent freshwaters independently, considering the different freshwater ecoregions.
##### ##### ##### ##### Loading data ##### ##### ##### #####
load("Paisajes_Ensamble_Europa.RData")
# Complete matrix with all the values for each freshwater type: EF(1).T(2).P(3) and Land (0)
M.final.UK # Values obtained for the Ecoregion corresponding to the UK
# Different countries/ecoregions can be obtained
unique(M.final.UK$ISO3_CODE);dim(M.final.UK)
unique(M.final.SWE$ISO3_CODE); dim(M.final.SWE)
unique(M.final.FIN$ISO3_CODE)
unique(M.final_FRA.LUX.BEL.NLD$ISO3_CODE)
unique(M.final.NOR$ISO3_CODE)
unique(M.final.FW.UK$ISO3_CODE)
unique(M.final.FW.SWE$ISO3_CODE)
unique(M.final.FW.ESP.PRT$ISO3_CODE)
unique(M.final.FW.FIN$ISO3_CODE)
unique(M.final.FW_FRA.LUX.BEL.NLD$ISO3_CODE)
unique(M.final.FW.NOR$ISO3_CODE)All freshwaters
InDegree
“SINK-MASS EFECT (in-degree; 4Km)”
It reflects the importance of incoming dispersal from other communities for local diversity, is estimated as the sum of all links arriving at the reference cell.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# All freshwaters: EF(1).T(2).P(3) == 0 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="All-freshwater (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.FW.UK->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## SWE
M.final.FW.SWE->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## ESP.PRT
M.final.ESP.PRT->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## NOR
M.final.FW.NOR->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## FIN
M.final.FW.FIN->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.in.D50.4),
max(B$grado.in.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)OutDegree
“SOURCE EFECT (in-degree; 4Km)”
It reflects the potential of a node (local communities) to operate as a source community is the sum of link weights along all the links that start on the reference cell.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# All freshwaters: EF(1).T(2).P(3) == 0 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="All-freshwater (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.FW.UK->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## SWE
M.final.FW.SWE->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## ESP.PRT
M.final.ESP.PRT->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## FIN
M.final.FIN->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## NOR
M.final.NOR->B
ii <- cut(B$grado.in.D50.4,
breaks = seq(min(B$grado.out.D50.4),
max(B$grado.out.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)Betweenness
“STEPPING STONE (BC-4Km)”
Communities importance for connecting other communities (corridor effects) is captured by the graph centrality metric ‘betweenness’. This metric indicates the number of pairs of other communities that pass through this community in the shortest path that connects them.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# All freshwaters: EF(1).T(2).P(3) == 0 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="All-freshwater (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.FW.UK->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## SWE
M.final.FW.SWE->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4,col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## ESP.PRT
M.final.ESP.PRT->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4, col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
## NOR
M.final.NOR->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4, col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
##FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4, col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
##FIN
M.final.FIN->B
ii <- cut(B$bc.D50.4,
breaks = seq(min(B$bc.D50.4),
max(B$bc.D50.4), len = 600), include.lowest = TRUE)
points(B$CENTROID_Y~B$CENTROID_X,cex=0.4, col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,B)
Ephemeral, Temporal and Permanent
InDegree
“SINK-MASS EFECT (in-degree; 4Km)”
It reflects the importance of incoming dispersal from other communities for local diversity, is estimated as the sum of all links arriving at the reference cell.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Ephenmeral freshwaters: EF(1).T(2).P(3) == 1 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Ephemeral (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="dark gray",pch=15)
mtext("Mass effect \n (in-degree)", outer = TRUE, cex = 1.5,padj = 0,col="black")
## UK
M.final.UK->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###SWE
M.final.SWE->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###ESP.PRT
M.final.ESP.PRT->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
M.final.FIN->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
M.final_FRA.LUX.BEL.NLD->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
M.final.NOR->A
ii <- cut(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.in.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Temporal freshwaters: EF(1).T(2).P(3) == 2 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Temporal (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## SWE
M.final.SWE->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## ESP.PRT
M.final.ESP.PRT->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## FIN
M.final.FIN->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## NOR
M.final.NOR->AA
ii <- cut(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.in.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Permanent freshwaters: EF(1).T(2).P(3) == 3 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Permanent (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## SWE
M.final.SWE->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## ESP.PRT
M.final.ESP.PRT->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FIN
M.final.FIN->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## NOR
M.final.NOR->AAA
ii <- cut(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.in.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)OutDegree
“SOURCE EFECT (in-degree; 4Km)”
It reflects the potential of a node (local communities) to operate as a source community is the sum of link weights along all the links that start on the reference cell.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Ephemeral freshwaters: EF(1).T(2).P(3) == 1 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Ephemeral (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="dark gray",pch=15)
mtext("Source patches \n (out-degree)", outer = TRUE, cex = 1.5,padj = 0,col="black")
## UK
M.final.UK->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###SWE
M.final.SWE->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###ESP.PRT
M.final.ESP.PRT->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###FIN
M.final.FIN->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###NOR
M.final.NOR->A
ii <- cut(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$grado.out.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Temporal freshwaters: EF(1).T(2).P(3) == 2 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Temporal (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## SWE
M.final.SWE->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## ESP.PRT
M.final.ESP.PRT->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## FIN
M.final.FIN->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## NOR
M.final.NOR->AA
ii <- cut(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$grado.out.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Permanent freshwaters: EF(1).T(2).P(3) == 3 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Permanent (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## SWE
M.final.SWE->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## ESP.PRT
M.final.ESP.PRT->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FIN
M.final.FIN->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## NOR
M.final.NOR->AAA
ii <- cut(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$grado.out.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)Betweenness
“STEPPING STONE (BC-4Km)”
Communities importance for connecting other communities (corridor effects) is captured by the graph centrality metric ‘betweenness’. This metric indicates the number of pairs of other communities that pass through this community in the shortest path that connects them.
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Ephemeral freshwaters: EF(1).T(2).P(3) == 1 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Ephemeral (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="dark gray",pch=15)
mtext("Stepping stone patches \n (betweenness)", outer = TRUE, cex = 1.5,padj = 0,col="black")
## UK
M.final.UK->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###SWE
M.final.SWE->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###ESP.PRT
M.final.ESP.PRT->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###NOR
M.final.NOR->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
###FIN
M.final.FIN->A
ii <- cut(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)],
breaks = seq(min(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]),
max(A$bc.D50.4[which(A$`EF(1).T(2).P(3)`==1)]), len = 600), include.lowest = TRUE)
points(A$CENTROID_Y[which(A$`EF(1).T(2).P(3)`==1)]~A$CENTROID_X[which(A$`EF(1).T(2).P(3)`==1)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,A)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Temporal freshwaters: EF(1).T(2).P(3) == 2 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Temporal (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## SWE
M.final.SWE->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## ESP.PRT
M.final.ESP.PRT->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## NOR
M.final.NOR->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## M.final_FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
## FIN
M.final.FIN->AA
ii <- cut(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)],
breaks = seq(min(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]),
max(AA$bc.D50.4[which(AA$`EF(1).T(2).P(3)`==2)]), len = 600), include.lowest = TRUE)
points(AA$CENTROID_Y[which(AA$`EF(1).T(2).P(3)`==2)]~AA$CENTROID_X[which(AA$`EF(1).T(2).P(3)`==2)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AA)
par(mar=c(2.5,2.5,1.5,1.5),bty="l",cex=1.6)
par(mfrow=c(1,1),oma = c(0, 0, 4, 0))
# Permanent freshwaters: EF(1).T(2).P(3) == 3 ____ ####
plot(M.Europa.J$CENTROID_Y~M.Europa.J$CENTROID_X,cex=0.1,col="light gray",pch=15, main="Permanent (4Km)")
points(M.Europa.J$CENTROID_Y[which(M.Europa.J$ISO3_CODE=="")]~M.Europa.J$CENTROID_X[which(M.Europa.J$ISO3_CODE=="")],cex=0.1,col="black",pch=15)
## UK
M.final.UK->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## SWE
M.final.SWE->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## ESP.PRT
M.final.ESP.PRT->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FIN
M.final.FIN->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## NOR
M.final.NOR->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
## FRA.LUX.BEL.NLD
M.final_FRA.LUX.BEL.NLD->AAA
ii <- cut(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)],
breaks = seq(min(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]),
max(AAA$bc.D50.4[which(AAA$`EF(1).T(2).P(3)`==3)]), len = 600), include.lowest = TRUE)
points(AAA$CENTROID_Y[which(AAA$`EF(1).T(2).P(3)`==3)]~AAA$CENTROID_X[which(AAA$`EF(1).T(2).P(3)`==3)],cex=0.4,
col = colorRampPalette(c("yellow", "orange", "red"))(599)[ii],pch=15)
rm(ii,AAA)
Log-Ratio plots
Then, we estimated the log-ratio of each centrality metric (CentralityLR) between each pair of water habitat (i.e. permanent vs. temporary, permanent vs. ephemeral and temporary vs. ephemeral) as an index of the relative importance of the potential routes of dispersal between different habitats—e. g. BetweennessLR = log10(Betweennesstemporal/ Betweennesspermanent) (see Riibak et al., 2017 for a log-ratio-based analysis). To this aim, the centrality metrics were standardized between 0 and 1 within each freshwater ecoregion to make them directly comparable. Large positive or negative log-ratios indicate that one specific area could be more important in promoting freshwater connectivity for one type of freshwater habitat than for other. Log ratios close to zero indicate that both areas are similarly important for the connectivity of the two compared habitats. For the log-ratio estimations, only cells that had at least two types of water habitats were included.
